ISPda1

  • Family IS1
  • Group
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
KP100338 ND Photobacterium damselae
Photobacterium damselae
Photobacterium damselae subsp. piscicida plasmid pPHDP70
Photobacterium damselae subsp. piscicida strain DI21 genome
Photobacterium damselae subsp. piscicida strain L091106-03H genome
DNA section
IS Length : 780 bp

Ends


IR Length : 29/35

IRL : GGTAGTGACCCCAATTGATTTATTTAGTATATAATCATCCTTTTTAAGGA
IRR : GGTGGTGACTCCAATTGATTTATTAATGGTAAAATTCACGTTCTATAAAC

Insertion site


Left flankDirect repeatRight flankDR Length
GGAATTTCAATTCCTAACCATAATACCTGTAAGAGTAAAC0
AAGTGTGGTGCTGATTTATCTCTAAAAAATAT8
ATACTTAACATCAAAAGATGGGATTTGGTCAACACAATGT0
TCTGTTCTGGGCCTTTTTTGCCATATAGTGGATAGGTTAC0

DNA sequence

GGTAGTGACCCCAATTGATTTATTTAGTATATAATCATCCTTTTTAAGGATGGATTATTCATGGCTACTATTGATGTGAAATGTCGTTTTTGTAATCAAG
CGGAGCAAGTCCGCAAATATGGGACTAATCCACGAGGAGCTCAGCGATATCGCTGCTTTGATTGCAATCGAACATTTCTTCTTGATTACGCTTATGAAGC
TTGTAAACCTGGCGTTAAGGAAAAGATTGTTGATATGGCGATGAATAGTTCAGGAGTAAGAGAGACGGGTCGAGTTTTGAAAGTCGGCTATAATACAGTA
CTACGCACTTTAAAAAACTCACACCGAAGCAAGTAACAACAATTCCCTTTGATATAGCCCACATTGAACTGATATGTGAAGTTGATGAGCAATGGTCGTT
TGTCGGTAAAAAAAAGAATCAGCGCTGGTTATGGTATGCGTGGGAACCTAGATATAAGCGAGTCATTGCTCATGTATTTGGGAAACGGGACTCAGAAACA
TTCCATAAACTCCAACGTCTTCTTTTGCCGTTTACTATTCCTATTTATTGCACAGATGATTTTAAGGTGTATTCAAGCTATTTACCAAGAGAAAATCACA
TCATAGGTAAGCGATACACGCAACGAATTGAAAGAACAAATTTAACATTACGATCTCGACTAAAAAGATTAGTAAGAAAAACCATTGGTTTTTCGAAAAG
CGAAGAGATGCACGATAAGGTTATTGGAACGTTTATAGAACGTGAATTTTACCATTAATAAATCAATTGGAGTCACCACC
Recoding section
  • Recoding by frameshift
  • Frame -1
  • Type translational
  • Experimentally demonstrated No

Stimulators :

  • Shine-Dalgarno sequence : No
  • Secondary structure : No-structure

Recoding motif :

CTACGCACTTTAAAAAACTCACACCGAAGCAAGTAA
........----------..................
Protein section
ORF number : 3

 

ORF 1
LengthBeginEndStrandFusion ORF
276 bp91 aa61336+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MATIDVKCRFCNQAEQVRKYGTNPRGAQRYRCFDCNRTFLLDYAYEACKPGVKEKIVDMAMNSSGVRETGRVLKVGYNTVLRTLKNSHRSK

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
465 bp154 aa294758+No
ORF function : Transposase
Chemistry : Unknow

ORF sequence :

YSTTHFKKLTPKQVTTIPFDIAHIELICEVDEQWSFVGKKKNQRWLWYAWEPRYKRVIAHVFGKRDSETFHKLQRLLLPFTIPIYCTDDFKVYSSYLPRE
NHIIGKRYTQRIERTNLTLRSRLKRLVRKTIGFSKSEEMHDKVIGTFIEREFYH

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
698 bp232 aa61758+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MATIDVKCRFCNQAEQVRKYGTNPRGAQRYRCFDCNRTFLLDYAYEACKPGVKEKIVDMAMNSSGVRETGRVLKVGYNTVLRTLKKLTPKQVTTIPFDIA
HIELICEVDEQWSFVGKKKNQRWLWYAWEPRYKRVIAHVFGKRDSETFHKLQRLLLPFTIPIYCTDDFKVYSSYLPRENHIIGKRYTQRIERTNLTLRSR
LKRLVRKTIGFSKSEEMHDKVIGTFIEREFYH

 

Blast result :
Comments
ISPda1 is 81% aa similar to ISVvu1. The third ORF is the putative ORFAB transposase reconstructed in silico by possible -1 frameshift.
References
1] Osorio, C.R., Rivas, A.J., Balado, M., Fuentes-Monteverde, J.C., Rodríguez, J., Jiménez, C., Lemos, M.L., Waldor, M.K., (2015) Appl. Environ. Microbiol. 81, 5867–5879. doi:10.1128/AEM.01580-15